GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Shewanella oneidensis MR-1

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate 202599 SO3496 aldehyde dehydrogenase (NCBI ptt file)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_495
         (480 letters)



>FitnessBrowser__MR1:202599
          Length = 498

 Score =  280 bits (717), Expect = 6e-80
 Identities = 166/472 (35%), Positives = 263/472 (55%), Gaps = 10/472 (2%)

Query: 12  QAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPA--WRALTA 69
           +AFI+G + DA +G T    +P  G +L  V      +   A+  A +   +  W     
Sbjct: 22  KAFINGEYRDASSGNTFDCISPIDGRLLAPVASCDLMDANIAVANAREVFDSGVWSKAAP 81

Query: 70  KERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKG-EIVYAASFIEWFAEEAKRIYG 128
            +R   + R+ EL+ EN ++LA L TL+ GKP+  +K  ++  AA  I W  E   ++Y 
Sbjct: 82  VKRKQVMIRFAELLEENANELALLETLDMGKPIRFSKAVDVAGAARAIRWSGEAIDKLYD 141

Query: 129 DVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFS 188
           ++ P    +  +I  ++P+GV AAI PWNFP  M   K GPAL  G +++LKP+ ++P +
Sbjct: 142 ELAPTAHNEIGMIT-REPVGVVAAIVPWNFPLLMACWKLGPALVTGNSVILKPSEKSPLT 200

Query: 189 AFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAK- 247
           A  +AELA +AGIP GV +V+ G    +G  L  +  V  L FTGST+I +QLM    + 
Sbjct: 201 AIRIAELAVQAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGES 260

Query: 248 DIKKVSLELGGNAPFIVFDDA-DLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFA 306
           ++K+V LE GG +P IVF+DA DL  A   A  +   N G+ C   +RL ++ GV D   
Sbjct: 261 NMKRVWLEAGGKSPNIVFNDAPDLKAAAVAAAEAIGFNQGEVCTAGSRLLVESGVKDELV 320

Query: 307 EKLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM----E 362
             +   +A  + G+ LE  T +G ++D++ +  +  +I    ++GA+++ GG+ +     
Sbjct: 321 GLIAEELASWQPGHPLEPTTVSGAVVDKQQLDTILSYIKAGQNEGASLVYGGQQVLAETG 380

Query: 363 GNFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLG 422
           G + +PT+ +NV N   +A EE FGP+  +  F    + IA++NDT +GLA+  +  D+ 
Sbjct: 381 GVYVQPTVFSNVKNQMKIASEEIFGPVLSVIEFNGMEEAIAIANDTIYGLAAGVWTADIS 440

Query: 423 RVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474
           +  + A+AL  GMV +N     +  APFGG K SG GR+ S +  + Y EIK
Sbjct: 441 KAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHSFDKYTEIK 492


Lambda     K      H
   0.317    0.135    0.390 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 569
Number of extensions: 23
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 480
Length of database: 498
Length adjustment: 34
Effective length of query: 446
Effective length of database: 464
Effective search space:   206944
Effective search space used:   206944
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory